Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells

Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5–SMG7 and SMG6

(2014) Sutapa Chakrabarti et al.   NUCLEIC ACIDS RESEARCH

3′ UTR Length and Messenger Ribonucleoprotein Composition Determine Endocleavage Efficiencies at Termination Codons

(2014) Volker Boehm et al.   Cell Reports

Organizing Principles of Mammalian Nonsense-Mediated mRNA Decay

(2013) Maximilian Wei-Lin Popp et al.   Annual Review of Genetics

Nonsense-mediated mRNA decay — Mechanisms of substrate mRNA recognition and degradation in mammalian cells

(2013) Christoph Schweingruber et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The SMG5-SMG7 heterodimer directly recruits the CCR4-NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2

(2013) B. Loh et al.   GENES & DEVELOPMENT

The role of disordered protein regions in the assembly of decapping complexes and RNP granules

(2013) S. Jonas et al.   GENES & DEVELOPMENT

The UPF3B gene, implicated in intellectual disability, autism, ADHD and childhood onset schizophrenia regulates neural progenitor cell behaviour and neuronal outgrowth

(2013) Lachlan A. Jolly et al.   HUMAN MOLECULAR GENETICS

Expression of new antigens on tumor cells by inhibiting nonsense-mediated mRNA decay

(2013) Eli Gilboa   IMMUNOLOGIC RESEARCH

Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates

(2013) Arnaldo L. Schapire et al.   METHODS

Comprehensive Investigation of MicroRNAs Enhanced by Analysis of Sequence Variants, Expression Patterns, ARGONAUTE Loading, and Target Cleavage

(2013) D.-H. Jeong et al.   PLANT PHYSIOLOGY

SMG6 Cleavage Generates Metastable Decay Intermediates from Nonsense-Containing β-Globin mRNA

(2013) Roshan Mascarenhas et al.   PLoS One

Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways

(2013) S. Metze et al.   RNA

Staufen-mediated mRNA decay

(2013) Eonyoung Park et al.   Wiley Interdisciplinary Reviews-RNA

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

(2013) Dong-Hoon Jeong et al.   GENOME BIOLOGY

A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon

(2013) Jingyu Zhang et al.   GENOME BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Ataluren as an Agent for Therapeutic Nonsense Suppression

(2012) Stuart W. Peltz et al.   Annual Review of Medicine

Methods for validation of miRNA sequence variants and the cleavage of their targets

(2012) Dong-Hoon Jeong et al.   METHODS

NMD: a multifaceted response to premature translational termination

(2012) Stephanie Kervestin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SMG5–PNRC2 is functionally dominant compared with SMG5–SMG7 in mammalian nonsense-mediated mRNA decay

(2012) Hana Cho et al.   NUCLEIC ACIDS RESEARCH

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

(2012) Y. Harigaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA surveillance is required for endoplasmic reticulum homeostasis

(2012) K. Sakaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability

(2012) Hidenori Tani et al.   RNA Biology

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

RNA Homeostasis Governed by Cell Type-Specific and Branched Feedback Loops Acting on NMD

(2011) Lulu Huang et al.   MOLECULAR CELL

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

(2011) Cameron P. Bracken et al.   NUCLEIC ACIDS RESEARCH

N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD

(2011) Yukiko Okada-Katsuhata et al.   NUCLEIC ACIDS RESEARCH

Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories

(2011) L. A. Rymarquis et al.   RNA

Autoregulation of the nonsense-mediated mRNA decay pathway in human cells

(2011) H. Yepiskoposyan et al.   RNA

SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay

(2010) I. Kashima et al.   GENES & DEVELOPMENT

Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay

(2010) Fernando Pastor et al.   NATURE

How and where are nonsense mRNAs degraded in mammalian cells?

(2010) Oliver Mühlemann et al.   RNA Biology

Human Proline-Rich Nuclear Receptor Coregulatory Protein 2 Mediates an Interaction between mRNA Surveillance Machinery and Decapping Complex

(2009) Hana Cho et al.   MOLECULAR CELL

Mutations of the UPF3B gene, which encodes a protein widely expressed in neurons, are associated with nonspecific mental retardation with or without autism

(2009) F Laumonnier et al.   MOLECULAR PSYCHIATRY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

Hypoxic Inhibition of Nonsense-Mediated RNA Decay Regulates Gene Expression and the Integrated Stress Response

(2008) L. B. Gardner   MOLECULAR AND CELLULAR BIOLOGY

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

The multiple lives of NMD factors: balancing roles in gene and genome regulation

(2008) Olaf Isken et al.   NATURE REVIEWS GENETICS

SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells

(2008) Andrea B Eberle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptome-Wide Analysis of Uncapped mRNAs in Arabidopsis Reveals Regulation of mRNA Degradation

(2008) Y. Jiao et al.   PLANT CELL

SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan

(2008) E. Huntzinger et al.   RNA

A Competition between Stimulators and Antagonists of Upf Complex Recruitment Governs Human Nonsense-Mediated mRNA Decay

(2008) Guramrit Singh et al.   PLOS BIOLOGY

Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region

(2008) Andrea B Eberle et al.   PLOS BIOLOGY